[R] Error in evalauating a function

[Martin Morgan]

On 08/30/2011 04:19 PM, Debs Majumdar wrote:
> Here's the plik code I ran:
>
> plink --bfile olr_try1 --pheno p3.txt --pheno-name dnum --covar p3.txt --covar-name a4 --missing-phenotype -9 --R olr2.R
>
> The below function is contained in the olr2.R script.
>
> The data which I input is contained in the binary file named olr_try1.
> The response variable (PHENO) and the covariate (COVAR) is contained in the file p3.txt.
>
> I added the option --R-debug to get the output below.
>
>   Thanks,
>
>   Debs
>
>
>
>
> ----- Original Message -----
> From: Debs Majumdar<debs_stata at yahoo.com>
> To: "r-help at r-project.org"<r-help at r-project.org>
> Cc:
> Sent: Tuesday, August 30, 2011 3:49 PM
> Subject: Error in evalauating a function
>
> Hi,
>
>
>    I am very new to R. So, pardon my dumb question. I was trying to write my own function to run a different model (perform an ordered logistic regression) using the example in website http://pngu.mgh.harvard.edu/~purcell/plink/rfunc.shtml
>
> But R returns a error `R Error in eval(expr, envir, enclos) : object 's' not found' when I run it. What am I doing wrong here? Here's what I got from the debug file.
>
> # Input data
>
> n<- 10
> PHENO<- c( 1, 3, 2, 3, 1, 1, 1, 2, 1, 2 )
> c<- c( 1, 1, 0, 0, 0, 0, 0, 1, 0, 0 )
> COVAR<- matrix( c , nrow = n , byrow=T)
> CLUSTER<- c( 0, 0, 0, 0, 0, 0, 0, 0, 0, 0 )
> l<- 22
> g<- c( 0, 1, 1, 0, 0, 0, 1, 0, 2, 1, 0, 0, 0, 0, 0, 1, 1, 1, 0, 1, 0, 0, 1, 2, 0, 0, 0, 2, 0, 0, 0, 1, 0, 1, 0, 1, 0, 1, 0, 2, 0, 1, 1, 0, 1, 0, 0, 1, 0, 0, 0, 0, 0, 1, 0, 0, 1, 1, -1, -1, 1, 0, 0, 1, 1, -1, 1, 0, 1, 0, 0, 2, 0, 0, 0, 1, 0, 0, 0, 0, 0, 1, 0, 1, 0, 0, 0, 0, 1, 2, 0, 1, 0, 0, 1, 0, 1, 0, 1, 2, 0, 1, 1, 0, 1, 0, 2, 1, 0, 0, 0, 2, 1, 0, 1, 0, 1, 0, 1, 0, 0, 1, 0, 0, 0, 0, 0, 0, 1, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 2, 0, 0, -1, -1, 0, 1, 0, 0, 0, 2, 0, 1, 0, 0, 0, 2, 0, 1, 1, 2, 0, 0, 1, 0, 1, -1, 0, 0, 0, 1, 0, 0, 0, 1, 0, 0, 1, 0, 1, 0, 0, 0, 1, 0, 1, 0, 0, 1, 0, 1, 0, 1, 0, 1, 0, 2, 0, 1, 1, 0, 0, 1, 1, 1, 0, 0, 0, 0, 1, 1, 2, 0, 0, 0, 1, 1, 1, 0, 0 )
> GENO<- matrix( g , nrow = n ,byrow=T)
> GENO[GENO == -1 ]<- NA
>
>
> # Function
>
> library(ordinal)
>       Rplink<- function(PHENO,GENO,CLUSTER,COVAR)
>       {
>        f1<- function(s)
>        {
>          m<- summary(clm(PHENO ~ s))

I see the error if I run the command

   Rplink(PHENO, GENO, CLUSTER, COVAR)

after sourcing the code you provided. I think clm is not implemented 
correctly; it is looking for 's' in the wrong environment. Help it along 
by providing an explicit 'data' argument. Also, PHENO is apparently 
supposed to be a 'factor'. So maybe replace the previous line with...

         df <- data.frame(PHENO=factor(PHENO), s)
         m <- summary(clm(PHENO ~ s, data=df))

Perhaps contact the maintainer of the 'ordinal' package (use 
packageDescription('ordinal') to report the issue.

Martin

>          r<- c(m$coef)
>          c( length(r) , r )
>        }
>       apply( GENO , 2 , f1 )
>       }
>
>
> Thanks,
>
>   Debs
>
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